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Bukowska-Olech E, Majchrzak-Celińska A, Przyborska M, Jamsheer A. Chromatinopathies: insight in clinical aspects and underlying epigenetic changes. J Appl Genet 2024; 65:287-301. [PMID: 38180712 PMCID: PMC11003913 DOI: 10.1007/s13353-023-00824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Chromatinopathies (CPs), a group of rare inborn defects characterized by chromatin state imbalance, have evolved from initially resembling Cornelia de Lange syndrome to encompass a wide array of genetic diseases with diverse clinical presentations. The CPs classification now includes human developmental disorders caused by germline mutations in epigenes, genes that regulate the epigenome. Recent advances in next-generation sequencing have enabled the association of 154 epigenes with CPs, revealing distinctive DNA methylation patterns known as episignatures.It has been shown that episignatures are unique for a particular CP or share similarities among specific CP subgroup. Consequently, these episignatures have emerged as promising biomarkers for diagnosing and treating CPs, differentiating subtypes, evaluating variants of unknown significance, and facilitating targeted therapies tailored to the underlying epigenetic dysregulation.The following review was conducted to collect, summarize, and analyze data regarding CPs in such aspects as clinical evaluation encompassing long-term patient care, underlying epigenetic changes, and innovative molecular and bioinformatic methodologies that have been devised for the assessment of CPs. We have also shed light on promising novel treatment options that have surfaced in recent research and presented a synthesis of ongoing clinical trials, contributing to the current understanding of the dynamic and evolving nature of CPs investigation.
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Affiliation(s)
| | | | | | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
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Nava AA, Arboleda VA. The omics era: a nexus of untapped potential for Mendelian chromatinopathies. Hum Genet 2024; 143:475-495. [PMID: 37115317 PMCID: PMC11078811 DOI: 10.1007/s00439-023-02560-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
The OMICs cascade describes the hierarchical flow of information through biological systems. The epigenome sits at the apex of the cascade, thereby regulating the RNA and protein expression of the human genome and governs cellular identity and function. Genes that regulate the epigenome, termed epigenes, orchestrate complex biological signaling programs that drive human development. The broad expression patterns of epigenes during human development mean that pathogenic germline mutations in epigenes can lead to clinically significant multi-system malformations, developmental delay, intellectual disabilities, and stem cell dysfunction. In this review, we refer to germline developmental disorders caused by epigene mutation as "chromatinopathies". We curated the largest number of human chromatinopathies to date and our expanded approach more than doubled the number of established chromatinopathies to 179 disorders caused by 148 epigenes. Our study revealed that 20.6% (148/720) of epigenes cause at least one chromatinopathy. In this review, we highlight key examples in which OMICs approaches have been applied to chromatinopathy patient biospecimens to identify underlying disease pathogenesis. The rapidly evolving OMICs technologies that couple molecular biology with high-throughput sequencing or proteomics allow us to dissect out the causal mechanisms driving temporal-, cellular-, and tissue-specific expression. Using the full repertoire of data generated by the OMICs cascade to study chromatinopathies will provide invaluable insight into the developmental impact of these epigenes and point toward future precision targets for these rare disorders.
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Affiliation(s)
- Aileen A Nava
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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Wei Y, Wang J, Qu R, Zhang W, Tan Y, Sha Y, Li L, Yin T. Genetic mechanisms of fertilization failure and early embryonic arrest: a comprehensive review. Hum Reprod Update 2024; 30:48-80. [PMID: 37758324 DOI: 10.1093/humupd/dmad026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/07/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND Infertility and pregnancy loss are longstanding problems. Successful fertilization and high-quality embryos are prerequisites for an ongoing pregnancy. Studies have proven that every stage in the human reproductive process is regulated by multiple genes and any problem, at any step, may lead to fertilization failure (FF) or early embryonic arrest (EEA). Doctors can diagnose the pathogenic factors involved in FF and EEA by using genetic methods. With the progress in the development of new genetic technologies, such as single-cell RNA analysis and whole-exome sequencing, a new approach has opened up for us to directly study human germ cells and reproductive development. These findings will help us to identify the unique mechanism(s) that leads to FF and EEA in order to find potential treatments. OBJECTIVE AND RATIONALE The goal of this review is to compile current genetic knowledge related to FF and EEA, clarifying the mechanisms involved and providing clues for clinical diagnosis and treatment. SEARCH METHODS PubMed was used to search for relevant research articles and reviews, primarily focusing on English-language publications from January 1978 to June 2023. The search terms included fertilization failure, early embryonic arrest, genetic, epigenetic, whole-exome sequencing, DNA methylation, chromosome, non-coding RNA, and other related keywords. Additional studies were identified by searching reference lists. This review primarily focuses on research conducted in humans. However, it also incorporates relevant data from animal models when applicable. The results were presented descriptively, and individual study quality was not assessed. OUTCOMES A total of 233 relevant articles were included in the final review, from 3925 records identified initially. The review provides an overview of genetic factors and mechanisms involved in the human reproductive process. The genetic mutations and other genetic mechanisms of FF and EEA were systematically reviewed, for example, globozoospermia, oocyte activation failure, maternal effect gene mutations, zygotic genome activation abnormalities, chromosome abnormalities, and epigenetic abnormalities. Additionally, the review summarizes progress in treatments for different gene defects, offering new insights for clinical diagnosis and treatment. WIDER IMPLICATIONS The information provided in this review will facilitate the development of more accurate molecular screening tools for diagnosing infertility using genetic markers and networks in human reproductive development. The findings will also help guide clinical practice by identifying appropriate interventions based on specific gene mutations. For example, when an individual has obvious gene mutations related to FF, ICSI is recommended instead of IVF. However, in the case of genetic defects such as phospholipase C zeta1 (PLCZ1), actin-like7A (ACTL7A), actin-like 9 (ACTL9), and IQ motif-containing N (IQCN), ICSI may also fail to fertilize. We can consider artificial oocyte activation technology with ICSI to improve fertilization rate and reduce monetary and time costs. In the future, fertility is expected to be improved or restored by interfering with or supplementing the relevant genes.
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Affiliation(s)
- Yiqiu Wei
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingxuan Wang
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rui Qu
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weiqian Zhang
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiling Tan
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanwei Sha
- Department of Andrology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Tailang Yin
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
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Effendi WI, Nagano T. Epigenetics Approaches toward Precision Medicine for Idiopathic Pulmonary Fibrosis: Focus on DNA Methylation. Biomedicines 2023; 11:biomedicines11041047. [PMID: 37189665 DOI: 10.3390/biomedicines11041047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Genetic information is not transmitted solely by DNA but by the epigenetics process. Epigenetics describes molecular missing link pathways that could bridge the gap between the genetic background and environmental risk factors that contribute to the pathogenesis of pulmonary fibrosis. Specific epigenetic patterns, especially DNA methylation, histone modifications, long non-coding, and microRNA (miRNAs), affect the endophenotypes underlying the development of idiopathic pulmonary fibrosis (IPF). Among all the epigenetic marks, DNA methylation modifications have been the most widely studied in IPF. This review summarizes the current knowledge concerning DNA methylation changes in pulmonary fibrosis and demonstrates a promising novel epigenetics-based precision medicine.
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Petroff RL, Cavalcante RG, Langen ES, Dolinoy DC, Padmanabhan V, Goodrich JM. Mediation effects of DNA methylation and hydroxymethylation on birth outcomes after prenatal per- and polyfluoroalkyl substances (PFAS) exposure in the Michigan mother-infant Pairs cohort. Clin Epigenetics 2023; 15:49. [PMID: 36964604 PMCID: PMC10037903 DOI: 10.1186/s13148-023-01461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/05/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFAS) are chemicals that are resistant to degradation and ubiquitous in our environments. PFAS may impact the developing epigenome, but current human evidence is limited to assessments of total DNA methylation. We assessed associations between first trimester PFAS exposures with newborn DNA methylation, including 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC). DNA methylation mediation of associations between PFAS and birth outcomes were explored in the Michigan Mother Infant Pairs cohort. Nine PFAS were measured in maternal first trimester blood. Seven were highly detected and included for analysis: PFHxS, PFOA, PFOS, PFNA, PFDA, PFUnDA, and MeFOSAA. Bisulfite-converted cord blood DNA (n = 141) and oxidative-bisulfite-converted cord blood (n = 70) were assayed on Illumina MethylationEPIC BeadChips to measure total DNA methylation (5-mC + 5-hmC) and 5-mC/5-hmC. Correcting for multiple comparisons, beta regressions were used to assess associations between levels of PFAS and total methylation, 5-mC, or 5-hmC. Nonlinear mediation analyses were used to assess the epigenetic meditation effect between PFAS and birth outcomes. RESULTS PFAS was significantly associated with total methylation (q < 0.05: PFHxS-12 sites; PFOS-19 sites; PFOA-2 sites; PFNA-3 sites; PFDA-4 sites). In 72 female infants and 69 male infants, there were sex-specific associations between five PFAS and DNA methylation. 5-mC and 5-hmC were each significantly associated with thousands of sites for PFHxS, PFOS, PFNA, PFDA, PFUnDA, and MeFOSAA (q < 0.05). Clusters of 5-mC and 5-hmC sites were significant mediators between PFNA and PFUnDA and decreased gestational age (q < 0.05). CONCLUSIONS This study demonstrates the mediation role of specific types of DNA methylation on the relationship between PFAS exposure and birth outcomes. These results suggest that 5-mC and 5-hmC may be more sensitive to the developmental impacts of PFAS than total DNA methylation.
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Affiliation(s)
- Rebekah L Petroff
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Raymond G Cavalcante
- Epigenomics Core, Biomedical Research Core Facilities, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Elizabeth S Langen
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
- Epigenomics Core, Biomedical Research Core Facilities, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pediatrics Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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Das U, Gangisetty O, Chaudhary S, Tarale P, Rousseau B, Price J, Frazier I, Sarkar DK. Epigenetic insight into effects of prenatal alcohol exposure on stress axis development: Systematic review with meta-analytic approaches. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2023; 47:18-35. [PMID: 36341762 DOI: 10.1111/acer.14972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
We conducted a systematic review with meta-analytic elements using publicly available Gene Expression Omnibus (GEO) datasets to determine the role of epigenetic mechanisms in prenatal alcohol exposure (PAE)-induced hypothalamic-pituitary-adrenal (HPA) axis dysfunctions in offspring. Several studies have demonstrated that PAE has long-term consequences on HPA axis functions in offspring. Some studies determined that alcohol-induced epigenetic alterations during fetal development persist in adulthood. However, additional research is needed to understand the major epigenetic events leading to alcohol-induced teratogenesis of the HPA axis. Our network analysis of GEO datasets identified key pathways relevant to alcohol-mediated histone modifications, DNA methylation, and miRNA involvement associated with PAE-induced alterations of the HPA axis. Our analysis indicated that PAE perturbated the epigenetic machinery to activate corticotrophin-releasing hormone, while it suppressed opioid, glucocorticoid receptor, and circadian clock genes. These results help to further our understanding of the epigenetic basis of alcohol's effects on HPA axis development.
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Affiliation(s)
- Ujjal Das
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Omkaram Gangisetty
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Shaista Chaudhary
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Prashant Tarale
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Bénédicte Rousseau
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Julianne Price
- Molecular Neuroscience of Alcohol and Drug Abuse Research Training, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center of Alcohol & Substance Use Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Department of Kinesiology & Health, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Ian Frazier
- Molecular Neuroscience of Alcohol and Drug Abuse Research Training, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center of Alcohol & Substance Use Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Department of Kinesiology & Health, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Dipak K Sarkar
- Endocrinology Program, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Molecular Neuroscience of Alcohol and Drug Abuse Research Training, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center of Alcohol & Substance Use Studies, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Rutgers Endocrinology Program, Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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Vetrivel S, Truong DJJ, Wurst W, Graw J, Giesert F. Identification of ocular regulatory functions of core histone variant H3.2. Exp Eye Res 2023; 226:109346. [PMID: 36529279 DOI: 10.1016/j.exer.2022.109346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/05/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The posttranscriptional modifications (PTM) of the Histone H3 family play an important role in ocular system differentiation. However, there has been no study on the nature of specific Histone H3 subtype carrying these modifications. Fortuitously, we had previously identified a dominant small-eye mutant Aey69 mouse with a mutation in the H3.2 encoding Hist2h3c1 gene (Vetrivel et al., 2019). In continuation, in the present study, the role of Histone H3.2 with relation to the microphtalmic Aey69 has been elaborated. Foremost, a transgenic mouse line expressing the fusion protein H3.2-GFP was generated using Crispr/Cas9. The approach was intended to confer a unique tag to the Hist2h3c1 gene which is similar in sequence and encoded protein structure to other histones. The GFP tag was then used for ChIP Seq analysis of the genes regulated by H3.2. The approach revealed ocular specific H3.2 targets including Ephrin family genes. Altered enrichment of H3.2 was found in the mutant Aey69 mouse, specifically around the ligand Efna5 and the receptor Ephb2. The effect of this altered enrichment on Ephrin signaling was further analysed by QPCR and immunohistochemistry. This study identifies Hist2h3c1 encoded H3.2 as an important epigenetic player in ocular development. By binding to specific regions of ocular developmental factors Histone H3.2 facilitates the function of these genes for successful early ocular development.
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Affiliation(s)
- Sharmilee Vetrivel
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany.
| | - Dong-Jiunn Jeffery Truong
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Jochen Graw
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany.
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Wang Z, Zheng H, Huang J, Yang G, Yan K, Zhang S, Wu C, Zheng C. DEMETHYLATION REGULATOR 1 regulates DNA demethylation of the nuclear and mitochondrial genomes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2344-2360. [PMID: 36223079 DOI: 10.1111/jipb.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Active DNA demethylation effectively modulates gene expression during plant development and in response to stress. However, little is known about the upstream regulatory factors that regulate DNA demethylation. We determined that the demethylation regulator 1 (demr1) mutant exhibits a distinct DNA methylation profile at selected loci queried by methylation-sensitive polymerase chain reaction and globally based on whole-genome bisulfite sequencing. Notably, the transcript levels of the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1) were lower in the demr1 mutant. We established that DEMR1 directly binds to the ROS1 promoter in vivo and in vitro, and the methylation level in the DNA methylation monitoring sequence of ROS1 promoter decreased by 60% in the demr1 mutant. About 40% of the hyper-differentially methylated regions (DMRs) in the demr1 mutant were shared with the ros1-4 mutant. Genetic analysis indicated that DEMR1 acts upstream of ROS1 to positively regulate abscisic acid (ABA) signaling during seed germination and seedling establishment stages. Surprisingly, the loss of DEMR1 function also caused a rise in methylation levels of the mitochondrial genome, impaired mitochondrial structure and an early flowering phenotype. Together, our results show that DEMR1 is a novel regulator of DNA demethylation of both the nuclear and mitochondrial genomes in response to ABA and plant development in Arabidopsis.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Hao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
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Zima L, West R, Smolen P, Kobori N, Hergenroeder G, Choi HA, Moore AN, Redell JB, Dash PK. Epigenetic Modifications and Their Potential Contribution to Traumatic Brain Injury Pathobiology and Outcome. J Neurotrauma 2022; 39:1279-1288. [PMID: 35481812 PMCID: PMC9529317 DOI: 10.1089/neu.2022.0128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epigenetic information is not permanently encoded in the DNA sequence, but rather consists of reversible, heritable modifications that regulate the gene expression profile of a cell. Epigenetic modifications can result in cellular changes that can be long lasting and include DNA methylation, histone methylation, histone acetylation, and RNA methylation. As epigenetic modifications are reversible, the enzymes that add (epigenetic writers), the proteins that decode (epigenetic readers), and the enzymes that remove (epigenetic erasers) these modifications can be targeted to alter cellular function and disease biology. While epigenetic modifications and their contributions are intense topics of current research in the context of a number of diseases, including cancer, inflammatory diseases, and Alzheimer disease, the study of epigenetics in the context of traumatic brain injury (TBI) is in its infancy. In this review, we will summarize the experimental and clinical findings demonstrating that TBI triggers epigenetic modifications, with a focus on changes in DNA methylation, histone methylation, and the translational utility of the universal methyl donor S-adenosylmethionine (SAM). Finally, we will review the evidence for using methyl donors as possible treatments for TBI-associated pathology and outcome.
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Affiliation(s)
- Laura Zima
- Department of Neurological Surgery, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Rebecca West
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Paul Smolen
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Nobuhide Kobori
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Georgene Hergenroeder
- Department of Neurological Surgery, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - HuiMahn A. Choi
- Department of Neurological Surgery, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Anthony N. Moore
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - John B. Redell
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Pramod K. Dash
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
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11
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Ishihara T, Hickford D, Fenelon JC, Griffith OW, Suzuki S, Renfree MB. Evolution of the short form of DNMT3A, DNMT3A2, occurred in the common ancestor of mammals. Genome Biol Evol 2022; 14:6615359. [PMID: 35749276 PMCID: PMC9254654 DOI: 10.1093/gbe/evac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is found in marsupial and eutherian mammals, but not in monotremes. While the primary regulator of genomic imprinting in eutherians is differential DNA methylation between parental alleles, conserved imprinted genes in marsupials tend to lack DNA methylation at their promoters. DNA methylation at eutherian imprinted genes is mainly catalysed by a DNA methyltransferase (DNMT) enzyme, DNMT3A. There are two isoforms of eutherian DNMT3A: DNMT3A and DNMT3A2. DNMT3A2 is the primary isoform for establishing DNA methylation at eutherian imprinted genes and is essential for eutherian genomic imprinting. In this study, we investigated whether DNMT3A2 is also present in the two other mammalian lineages, marsupials and monotremes. We identified DNMT3A2 in both marsupials and monotremes, although imprinting has not been identified in monotremes. By analysing genomic sequences and transcriptome data across vertebrates, we concluded that the evolution of DNMT3A2 occurred in the common ancestor of mammals. In addition, DNMT3A/3A2 gene and protein expression during gametogenesis showed distinct sexual dimorphisms in a marsupial, the tammar wallaby, and this pattern coincided with the sex-specific DNA methylation reprogramming in this species as it does in mice. Our results show that DNMT3A2 is present in all mammalian groups and suggests that the basic DNMT3A/3A2-based DNA methylation mechanism is conserved at least in therian mammals.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Danielle Hickford
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jane C Fenelon
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Oliver W Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Shinshu University, Nagano, Japan
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
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12
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Alagia A, Gullerova M. The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine. Front Cell Dev Biol 2022; 10:915685. [PMID: 35721489 PMCID: PMC9204050 DOI: 10.3389/fcell.2022.915685] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m5C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m5C deposition and removal, and the role m5C plays within the cell, remains to be fully understood.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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13
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Kaur P, Chaudhry C, Kaur A, Panigrahi I, Srivastava P. Case Studies of Two Classical Imprinting Growth Disorders: Silver–Russell and Beckwith–Wiedemann Syndromes. J Pediatr Genet 2021. [DOI: 10.1055/s-0041-1739388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractThe genetic influences on human growth are being increasingly deciphered. Silver–Russell and Beckwith–Wiedemann syndromes (SRS; BWS) are two relatively common genetic syndromes with under- and overgrowth-related issues being the reason for referral. Aberration in genomic imprinting is the underlying genetic pathomechanism behind these syndromes. Herein, we described a series of children with these two growth disorders and give an orientation to the reader of the concept of imprinting as well as the genetic testing strategy and counseling to be offered in these syndromes.
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Affiliation(s)
- Parminder Kaur
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Chakshu Chaudhry
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anupriya Kaur
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Priyanka Srivastava
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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14
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Li Y, Pollock CA, Saad S. Aberrant DNA Methylation Mediates the Transgenerational Risk of Metabolic and Chronic Disease Due to Maternal Obesity and Overnutrition. Genes (Basel) 2021; 12:genes12111653. [PMID: 34828259 PMCID: PMC8624316 DOI: 10.3390/genes12111653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/02/2021] [Accepted: 10/17/2021] [Indexed: 12/13/2022] Open
Abstract
Maternal obesity is a rapidly evolving universal epidemic leading to acute and long-term medical and obstetric health issues, including increased maternal risks of gestational diabetes, hypertension and pre-eclampsia, and the future risks for offspring's predisposition to metabolic diseases. Epigenetic modification, in particular DNA methylation, represents a mechanism whereby environmental effects impact on the phenotypic expression of human disease. Maternal obesity or overnutrition contributes to the alterations in DNA methylation during early life which, through fetal programming, can predispose the offspring to many metabolic and chronic diseases, such as non-alcoholic fatty liver disease, obesity, diabetes, and chronic kidney disease. This review aims to summarize findings from human and animal studies, which support the role of maternal obesity in fetal programing and the potential benefit of altering DNA methylation to limit maternal obesity related disease in the offspring.
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Affiliation(s)
- Yan Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China;
| | - Carol A. Pollock
- Kolling Institute of Medical Research, University of Sydney, Sydney, NSW 2065, Australia;
| | - Sonia Saad
- Kolling Institute of Medical Research, University of Sydney, Sydney, NSW 2065, Australia;
- Correspondence:
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15
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DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases. Int J Mol Sci 2021; 22:ijms221910540. [PMID: 34638881 PMCID: PMC8508711 DOI: 10.3390/ijms221910540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).
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16
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Deshpande SSS, Nemani H, Balasinor NH. High fat diet-induced- and genetically inherited- obesity differential alters DNA demethylation pathways in the germline of adult male rats. Reprod Biol 2021; 21:100532. [PMID: 34246869 DOI: 10.1016/j.repbio.2021.100532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
Obesity is a multifactorial condition with predominantly genetic and environmental causes and is an emerging risk factor for male infertility/subfertility. Epigenetic mechanisms are vulnerable to genetic and environmental changes. Our earlier studies have shown differential effects of genetically inherited (GIO) - and diet-induced- obesity (DIO) on DNA methylation in male germline. Contrary to DNA methylation is DNA demethylation, which also regulates the gene expression by activating transcription. The present study aimed to delineate the effects of obesity on the DNA demethylation pathway using two rat models: GIO (WNIN/Ob) and DIO (high-fat diet). We observed differential alterations in enzymes involved in DNA demethylation by oxidation (Tet1-3) pathway in testis in both groups. An increase in Tets in DIO group and a decrease in GIO group were noted. Analysis of oxidation pathway intermediates (5-hmC, 5-fC, and 5-caC) did not show any effect on testis in DIO group but an increase in 5-hmC and decrease in 5-caC levels in GIO group was observed. Analysis of transcript levels of enzymes related to deamination pathway in testis showed an increase (Gadd45a, Aicda, and Tdg) in DIO group and a decrease (Gadd45a, Aicda, and Tdg) in GIO group. Also, 5-hmC levels were differentially altered in the spermatozoa of both groups without any changes in Tet enzyme levels. These findings highlight differences in effects of GIO and DIO on DNA demethylation mechanisms in male germline, which could be due to differences in endocrine and metabolic profile as well as white fat distribution observed earlier in two groups.
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Affiliation(s)
- Sharvari S S Deshpande
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Harishankar Nemani
- National Institute of Nutrition Animal Facility, ICMR-National Institute of Nutrition, Jamai-Osmania PO, Hyderabad, 500 007, India
| | - Nafisa H Balasinor
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India.
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17
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Rygiel CA, Goodrich JM, Solano-González M, Mercado-García A, Hu H, Téllez-Rojo MM, Peterson KE, Dolinoy DC. Prenatal Lead (Pb) Exposure and Peripheral Blood DNA Methylation (5mC) and Hydroxymethylation (5hmC) in Mexican Adolescents from the ELEMENT Birth Cohort. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:67002. [PMID: 34152198 PMCID: PMC8216410 DOI: 10.1289/ehp8507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Gestational lead (Pb) exposure can adversely affect offspring health through multiple mechanisms, including epigenomic alterations via DNA methylation (5mC) and hydroxymethylation (5hmC), an intermediate in oxidative demethylation. Most current methods do not distinguish between 5mC and 5hmC, limiting insights into their individual roles. OBJECTIVE Our study sought to identify the association of trimester-specific (T1, T2, T3) prenatal Pb exposure with 5mC and 5hmC levels at multiple cytosine-phosphate-guanine sites within gene regions previously associated with prenatal Pb (HCN2, NINJ2, RAB5A, TPPP) in whole blood leukocytes of children ages 11-18 years of age. METHODS Participants from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) birth cohorts were selected (n=144) for pyrosequencing analysis following oxidative or standard sodium bisulfite treatment. This workflow directly quantifies total methylation (5mC+5hmC) and 5mC only; 5hmC is estimated by subtraction. RESULTS Participants were 51% male, and mean maternal blood lead levels (BLL) were 6.43±5.16μg/dL in Trimester 1 (T1), 5.66±5.21μg/dL in Trimester 2 (T2), and 5.86±4.34μg/dL in Trimester 3 (T3). In addition, 5hmC levels were calculated for HCN2 (mean±standard deviation(SD), 2.08±4.18%), NINJ2 (G/C: 2.01±5.95; GG: 0.90±3.97), RAB5A (0.66±0.80%), and TPPP (1.11±6.67%). Furthermore, 5mC levels were measured in HCN2 (81.3±9.63%), NINJ2 (heterozygotes: 38.6±7.39%; GG homozygotes: 67.3±9.83%), RAB5A (1.41±1.21%), and TPPP (92.5±8.03%). Several significant associations between BLLs and 5mC/5hmC were identified: T1 BLLs with 5mC in HCN2 (β=-0.37, p=0.03) and 5hmC in NINJ2 (β=0.49, p=0.003); T2 BLLs with 5mC in HCN2 (β=0.37, p=0.03) and 5hmC in NINJ2 (β=0.27, p=0.008); and T3 BLLs with 5mC in HCN2 (β=0.50, p=0.01) and NINJ2 (β=-0.35, p=0.004) and 5hmC in NINJ2 (β=0.45, p<0.001). NINJ2 5mC was negatively correlated with gene expression (Pearson r=-0.5, p-value=0.005), whereas 5hmC was positively correlated (r=0.4, p-value=0.04). DISCUSSION These findings suggest there is variable 5hmC in human whole blood and that prenatal Pb exposure is associated with gene-specific 5mC and 5hmC levels at adolescence, providing evidence to consider 5hmC as a regulatory mechanism that is responsive to environmental exposures. https://doi.org/10.1289/EHP8507.
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Affiliation(s)
- Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | | | | | - Howard Hu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Karen E. Peterson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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18
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Kim DY, Kim JM. Multi-omics integration strategies for animal epigenetic studies - A review. Anim Biosci 2021; 34:1271-1282. [PMID: 33902167 PMCID: PMC8255897 DOI: 10.5713/ab.21.0042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.
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Affiliation(s)
- Do-Young Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Korea
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19
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Perspectives for epigenetic editing in crops. Transgenic Res 2021; 30:381-400. [PMID: 33891288 DOI: 10.1007/s11248-021-00252-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.
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20
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Vural S, Palmisano A, Reinhold WC, Pommier Y, Teicher BA, Krushkal J. Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines. Clin Epigenetics 2021; 13:49. [PMID: 33676569 PMCID: PMC7936435 DOI: 10.1186/s13148-021-01026-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation may be associated with response of cancer cell lines to chemotherapy treatment with a variety of antitumor agents. RESULTS We analyzed 72 genes encoding epigenetic factors directly or indirectly involved in DNA methylation and demethylation processes. We examined association of their pretreatment expression levels with methylation beta-values of individual DNA methylation probes, DNA methylation averaged within gene regions, and average epigenome-wide methylation levels. We analyzed data from 645 cancer cell lines and 23 cancer types from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We observed numerous correlations between expression of genes encoding epigenetic factors and response to chemotherapeutic agents. Expression of genes encoding a variety of epigenetic factors, including KDM2B, DNMT1, EHMT2, SETDB1, EZH2, APOBEC3G, and other genes, was correlated with response to multiple agents. DNA methylation of numerous target probes and gene regions was associated with expression of multiple genes encoding epigenetic factors, underscoring complex regulation of epigenome methylation by multiple intersecting molecular pathways. The genes whose expression was associated with methylation of multiple epigenome targets encode DNA methyltransferases, TET DNA methylcytosine dioxygenases, the methylated DNA-binding protein ZBTB38, KDM2B, SETDB1, and other molecular factors which are involved in diverse epigenetic processes affecting DNA methylation. While baseline DNA methylation of numerous epigenome targets was correlated with cell line response to antitumor agents, the complex relationships between the overlapping effects of each epigenetic factor on methylation of specific targets and the importance of such influences in tumor response to individual agents require further investigation. CONCLUSIONS Expression of multiple genes encoding epigenetic factors is associated with drug response and with DNA methylation of numerous epigenome targets that may affect response to therapeutic agents. Our findings suggest complex and interconnected pathways regulating DNA methylation in the epigenome, which may both directly and indirectly affect response to chemotherapy.
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Affiliation(s)
- Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
- General Dynamics Information Technology (GDIT), 3150 Fairview Park Drive, Falls Church, VA, 22042, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Beverly A Teicher
- Molecular Pharmacology Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
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21
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Sedley L. Advances in Nutritional Epigenetics-A Fresh Perspective for an Old Idea. Lessons Learned, Limitations, and Future Directions. Epigenet Insights 2020; 13:2516865720981924. [PMID: 33415317 PMCID: PMC7750768 DOI: 10.1177/2516865720981924] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nutritional epigenetics is a rapidly expanding field of research, and the natural modulation of the genome is a non-invasive, sustainable, and personalized alternative to gene-editing for chronic disease management. Genetic differences and epigenetic inflexibility resulting in abnormal gene expression, differential or aberrant methylation patterns account for the vast majority of diseases. The expanding understanding of biological evolution and the environmental influence on epigenetics and natural selection requires relearning of once thought to be well-understood concepts. This research explores the potential for natural modulation by the less understood epigenetic modifications such as ubiquitination, nitrosylation, glycosylation, phosphorylation, and serotonylation concluding that the under-appreciated acetylation and mitochondrial dependant downstream epigenetic post-translational modifications may be the pinnacle of the epigenomic hierarchy, essential for optimal health, including sustainable cellular energy production. With an emphasis on lessons learned, this conceptional exploration provides a fresh perspective on methylation, demonstrating how increases in environmental methane drive an evolutionary down regulation of endogenous methyl groups synthesis and demonstrates how epigenetic mechanisms are cell-specific, making supplementation with methyl cofactors throughout differentiation unpredictable. Interference with the epigenomic hierarchy may result in epigenetic inflexibility, symptom relief and disease concomitantly and may be responsible for the increased incidence of neurological disease such as autism spectrum disorder.
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Affiliation(s)
- Lynda Sedley
- Bachelor of Health Science (Nutritional Medicine),
GC Biomedical Science (Genomics), The Research and Educational Institute of
Environmental and Nutritional Epigenetics, Queensland, Australia
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22
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MicroRNAs: Diverse Mechanisms of Action and Their Potential Applications as Cancer Epi-Therapeutics. Biomolecules 2020; 10:biom10091285. [PMID: 32906681 PMCID: PMC7565521 DOI: 10.3390/biom10091285] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022] Open
Abstract
Usually, miRNAs function post-transcriptionally, by base-pairing with the 3′UTR of target mRNAs, repressing protein synthesis in the cytoplasm. Furthermore, other regions including gene promoters, as well as coding and 5′UTR regions of mRNAs are able to interact with miRNAs. In recent years, miRNAs have emerged as important regulators of both translational and transcriptional programs. The expression of miRNA genes, similar to protein-coding genes, can be epigenetically regulated, in turn miRNA molecules (named epi-miRs) are able to regulate epigenetic enzymatic machinery. The most recent line of evidence indicates that miRNAs can influence physiological processes, such as embryonic development, cell proliferation, differentiation, and apoptosis as well as pathological processes (e.g., tumorigenesis) through epigenetic mechanisms. Some tumor types show repression of tumor-suppressor epi-miRs resulting in cancer progression and metastasis, hence these molecules have become novel therapeutic targets in the last few years. This review provides information about miRNAs involvement in the various levels of transcription and translation regulation, as well as discusses therapeutic potential of tumor-suppressor epi-miRs used in in vitro and in vivo anti-cancer therapy.
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23
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Wang B, Li R, Cai Y, Li B, Qin S, Zheng K, Zeng M, Xiao F, Zhang Z, Xu X. Alteration of DNA methylation induced by PM 2.5 in human bronchial epithelial cells. Toxicol Res (Camb) 2020; 9:552-560. [PMID: 32905279 PMCID: PMC7467236 DOI: 10.1093/toxres/tfaa061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/14/2020] [Accepted: 07/19/2020] [Indexed: 12/26/2022] Open
Abstract
This current study explored the effects of fine particulate matter (PM2.5) on deoxyribonucleic acid methylation in human bronchial epithelial cells. Human bronchial epithelial cells were exposed to PM2.5 for 24 h after which, deoxyribonucleic acid samples were extracted, and the differences between methylation sites were detected using methylation chips. Subsequent gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for the differential methylation sites. Functional epigenetic modules analysis of the overall differential methylation site interactions was also conducted. A total of 127 differential methylation sites in 89 genes were screened in the PM2.5 10 μg/ml group, of which 55 sites demonstrated increased methylation, with methylation levels decreasing in a further 72 sites. Following an exposure of 50 μg/ml PM2.5, a total of 238 differentially methylated sites were screened in 168 genes, of which methylation levels increased in 127 sites, and decreased in 111. KEGG analysis showed that the top 10 enrichment pathways predominantly involve hepatocellular carcinoma pathways and endometrial cancer pathways, whereas functional epigenetic modules analysis screened eight genes (A2M, IL23A, TPIP6, IL27, MYD88, ILE2B, NLRC4, TNF) with the most interactions. Our results indicate that exposure to PM2.5 for 24 h in human bronchial epithelial cells induces marked changes in deoxyribonucleic acid methylation of multiple genes involved in apoptosis and carcinogenesis pathways, these findings can provide a new direction for further study of PM2.5 carcinogenic biomarkers.
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Affiliation(s)
- Bingyu Wang
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Runbing Li
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Ying Cai
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Boru Li
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Shuangjian Qin
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Kai Zheng
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Ming Zeng
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Fang Xiao
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Zhaohui Zhang
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Xinyun Xu
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
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Syding LA, Nickl P, Kasparek P, Sedlacek R. CRISPR/Cas9 Epigenome Editing Potential for Rare Imprinting Diseases: A Review. Cells 2020; 9:cells9040993. [PMID: 32316223 PMCID: PMC7226972 DOI: 10.3390/cells9040993] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022] Open
Abstract
Imprinting diseases (IDs) are rare congenital disorders caused by aberrant dosages of imprinted genes. Rare IDs are comprised by a group of several distinct disorders that share a great deal of homology in terms of genetic etiologies and symptoms. Disruption of genetic or epigenetic mechanisms can cause issues with regulating the expression of imprinted genes, thus leading to disease. Genetic mutations affect the imprinted genes, duplications, deletions, and uniparental disomy (UPD) are reoccurring phenomena causing imprinting diseases. Epigenetic alterations on methylation marks in imprinting control centers (ICRs) also alters the expression patterns and the majority of patients with rare IDs carries intact but either silenced or overexpressed imprinted genes. Canonical CRISPR/Cas9 editing relying on double-stranded DNA break repair has little to offer in terms of therapeutics for rare IDs. Instead CRISPR/Cas9 can be used in a more sophisticated way by targeting the epigenome. Catalytically dead Cas9 (dCas9) tethered with effector enzymes such as DNA de- and methyltransferases and histone code editors in addition to systems such as CRISPRa and CRISPRi have been shown to have high epigenome editing efficiency in eukaryotic cells. This new era of CRISPR epigenome editors could arguably be a game-changer for curing and treating rare IDs by refined activation and silencing of disturbed imprinted gene expression. This review describes major CRISPR-based epigenome editors and points out their potential use in research and therapy of rare imprinting diseases.
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Affiliation(s)
- Linn Amanda Syding
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Nickl
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Correspondence: ; Tel.: +420-325-873-243
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Nutritional Factors Modulating Alu Methylation in an Italian Sample from The Mark-Age Study Including Offspring of Healthy Nonagenarians. Nutrients 2019; 11:nu11122986. [PMID: 31817660 PMCID: PMC6950565 DOI: 10.3390/nu11122986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/11/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
Alu hypomethylation promotes genomic instability and is associated with aging and age-related diseases. Dietary factors affect global DNA methylation, leading to changes in genomic stability and gene expression with an impact on longevity and the risk of disease. This preliminary study aims to investigate the relationship between nutritional factors, such as circulating trace elements, lipids and antioxidants, and Alu methylation in elderly subjects and offspring of healthy nonagenarians. Alu DNA methylation was analyzed in sixty RASIG (randomly recruited age-stratified individuals from the general population) and thirty-two GO (GeHA offspring) enrolled in Italy in the framework of the MARK-AGE project. Factor analysis revealed a different clustering between Alu CpG1 and the other CpG sites. RASIG over 65 years showed lower Alu CpG1 methylation than those of GO subjects in the same age class. Moreover, Alu CpG1 methylation was associated with fruit and whole-grain bread consumption, LDL2-Cholesterol and plasma copper. The preserved Alu methylation status in GO, suggests Alu epigenetic changes as a potential marker of aging. Our preliminary investigation shows that Alu methylation may be affected by food rich in fibers and antioxidants, or circulating LDL subfractions and plasma copper.
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26
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Urbano A, Smith J, Weeks RJ, Chatterjee A. Gene-Specific Targeting of DNA Methylation in the Mammalian Genome. Cancers (Basel) 2019; 11:cancers11101515. [PMID: 31600992 PMCID: PMC6827012 DOI: 10.3390/cancers11101515] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is the most widely-studied epigenetic modification, playing a critical role in the regulation of gene expression. Dysregulation of DNA methylation is implicated in the pathogenesis of numerous diseases. For example, aberrant DNA methylation in promoter regions of tumor-suppressor genes has been strongly associated with the development and progression of many different tumors. Accordingly, technologies designed to manipulate DNA methylation at specific genomic loci are very important, especially in the context of cancer therapy. Traditionally, epigenomic editing technologies have centered around zinc finger proteins (ZFP)- and transcription activator-like effector protein (TALE)-based targeting. More recently, however, the emergence of clustered regulatory interspaced short palindromic repeats (CRISPR)-deactivated Cas9 (dCas9)-based editing systems have shown to be a more specific and efficient method for the targeted manipulation of DNA methylation. Here, we describe the regulation of the DNA methylome, its significance in cancer and the current state of locus-specific editing technologies for altering DNA methylation.
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Affiliation(s)
- Arthur Urbano
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Jim Smith
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, 3A Symonds Street, Private Bag 92019, Auckland, New Zealand.
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27
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Ishihara T, Hickford D, Shaw G, Pask AJ, Renfree MB. DNA methylation dynamics in the germline of the marsupial tammar wallaby, Macropus eugenii. DNA Res 2019; 26:85-94. [PMID: 30535324 PMCID: PMC6379045 DOI: 10.1093/dnares/dsy040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/29/2018] [Indexed: 01/25/2023] Open
Abstract
Parent specific-DNA methylation is the genomic imprint that induces mono-allelic gene expression dependent on parental origin. Resetting of DNA methylation in the germ line is mediated by a genome-wide re-methylation following demethylation known as epigenetic reprogramming. Most of our understanding of epigenetic reprogramming in germ cells is based on studies in mice, but little is known about this in marsupials. We examined genome-wide changes in DNA methylation levels by measuring 5-methylcytosine expression, and mRNA expression and protein localization of the key enzyme DNA methyltransferase 3 L (DNMT3L) during germ cell development of the marsupial tammar wallaby, Macropus eugenii. Our data clearly showed that the relative timing of genome-wide changes in DNA methylation was conserved between the tammar and mouse, but in the tammar it all occurred post-natally. In the female tammar, genome-wide demethylation occurred in two phases, I and II, suggesting that there is an unidentified demethylation mechanism in this species. Although the localization pattern of DNMT3L in male germ cells differed, the expression patterns of DNMT3L were broadly conserved between tammar, mouse and human. Thus, the basic mechanisms of DNA methylation-reprogramming must have been established before the marsupial-eutherian mammal divergence over 160 Mya.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Danielle Hickford
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
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28
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Wang Q, Peng WX, Wang L, Ye L. Toward multiomics-based next-generation diagnostics for precision medicine. Per Med 2019; 16:157-170. [PMID: 30816060 DOI: 10.2217/pme-2018-0085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our healthcare system is experiencing a paradigm shift to precision medicine, aiming at an early prediction of individual disease risks and targeted interventions. Whole-genome sequencing is currently gaining momentum, as it has the potential to capture all classes of genetic variation, thus providing a more complete picture of the individual's genetic makeup, which could be utilized in genetic testing; however, this will also lead to difficulties in interpreting the test results, necessitating careful integration of genomic data with other layers of information, both molecular multiomics measurements of epigenome, transcriptome, proteome, metabolome and even microbiome, as well as comprehensive information on diet, lifestyle and environment. Overall, the translation of patient-specific data into actionable diagnostic tools will be a challenging task, requiring expertise from multiple disciplines, secure data sharing in large reference databases and a strong computational infrastructure.
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Affiliation(s)
- Qi Wang
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Wei-Xian Peng
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Lu Wang
- Department of Emergency Medicine, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang Province, China
| | - Li Ye
- Department of Nursing, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang Province, China
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29
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Muratori M, De Geyter C. Chromatin condensation, fragmentation of DNA and differences in the epigenetic signature of infertile men. Best Pract Res Clin Endocrinol Metab 2019; 33:117-126. [PMID: 30420311 DOI: 10.1016/j.beem.2018.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Epidemiological studies report an increase of pathologies of male reproductive tracts and suggest a link between this trend and the increased exposure of men to endocrine disruptors (EDs). The mechanisms by which EDs impact male fertility are far to be elucidated although DNA, chromatin and epigenome of spermatozoa appear to be relevant targets for these molecules. Indeed, many studies report associations between increased levels of sperm DNA fragmentation (sDF) or aberrant chromatin condensation or epigenetic modifications and poor semen quality and/or infertile phenotype. In this scenario, therapies able to reduce sperm damage to DNA, chromatin and epigenome are sought. Currently, antioxidants and FSH administration is proposed for treating high levels of sDF, but whether or not such therapies are really effective is still debated. Further studies are necessary to understand the link between endocrine disruptor exposure and damage to sperm function and/or structure and thus to define effective therapeutic strategies.
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Affiliation(s)
- Monica Muratori
- Department of Experimental, Clinical and Biomedical Sciences, Unit of Sexual Medicine and Andrology, Center of Excellence DeNothe, University of Florence, Viale Pieraccini, 6, I-50139, Firenze, Italy.
| | - Christian De Geyter
- Reproductive Medicine and Gynecological Endocrinology (RME), University Hospital, University of Basel, Vogesenstrasse 134, CH-4031, Basel, Switzerland.
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30
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Dynamic alterations in methylation of global DNA and growth-related genes in large yellow croaker (Larimichthys crocea) in response to starvation stress. Comp Biochem Physiol B Biochem Mol Biol 2019; 227:98-105. [DOI: 10.1016/j.cbpb.2018.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
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31
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Borroto-Escuela DO, Wydra K, Filip M, Fuxe K. A2AR-D2R Heteroreceptor Complexes in Cocaine Reward and Addiction. Trends Pharmacol Sci 2018; 39:1008-1020. [PMID: 30384981 DOI: 10.1016/j.tips.2018.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/10/2018] [Accepted: 10/08/2018] [Indexed: 12/29/2022]
Abstract
The concept of allosteric receptor-receptor interactions in G protein-coupled receptor homo- and heteroreceptor complexes in which they physically interact provides a new dimension to molecular integration in the brain. The receptor-receptor interactions dynamically change recognition, pharmacology, signaling, and trafficking of the participating receptors. Among the receptor complexes, disruption of the A2A receptor-dopamine D2 receptor (A2AR-D2R) complex by an A2AR agonist has been shown to fully block the inhibition of cocaine self-administration. Cocaine induced pathological A2AR-D2R-Sigma1R complexes may form a long-term memory with a strong and permanent D2R brake, leading to cocaine addiction. These heteroreceptor complexes can potentially be targeted for future pharmacotherapy of cocaine addiction by using heterobivalent compounds or A2AR-D2R receptor interface-interfering peptides that disrupt the A2AR-D2R-Sigma1R complexes.
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Affiliation(s)
| | - Karolina Wydra
- Institute of Pharmacology, Polish Academy of Sciences, Department of Drug Addiction Pharmacology, Smetna, Kraków, Poland
| | - Malgorzata Filip
- Institute of Pharmacology, Polish Academy of Sciences, Department of Drug Addiction Pharmacology, Smetna, Kraków, Poland
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institutet, Solnavägen 9, Stockholm, Sweden.
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32
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Iwagawa T, Watanabe S. Molecular mechanisms of H3K27me3 and H3K4me3 in retinal development. Neurosci Res 2018; 138:43-48. [PMID: 30227167 DOI: 10.1016/j.neures.2018.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 10/28/2022]
Abstract
The retina consists of six types of neuron and Müller glia, and they are individually derived from common retinal progenitors in a chronologically defined order. Therefore, the signaling environment and competency of retinal progenitors change during retinal development, and the retina serves as an excellent model system to analyze molecular events during development. Much attention has been given to the identification of transcription factors and epigenetic mechanisms. The dynamic changing of the histone modification levels of retina-specific genes has been observed, and the modification patterns of H3K4me3 and H3K27me3 are regulated in a retinal cell type-specific manner. Therefore, it appears that the dynamism of histone modification in the developing retina is regulated both chronologically and in a cell type-specific manner in a particular gene category. Loss- and gain-of-function analyses of enzymes involved in the methylation and demethylation of H3K4 and K27 in the retina have indicated their critical roles in proliferation, differentiation, and determinations of the timing for differentiation. We summarize recent findings related to the roles of H3K4me3 and H3K27me3 in retinal development to discuss how the retinal system provides intriguing data on and contributes to concepts regarding the roles of histone modification in the chronological regulation of tissue development.
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Affiliation(s)
- Toshiro Iwagawa
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
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33
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Biswas S, Rao CM. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. Eur J Pharmacol 2018; 837:8-24. [PMID: 30125562 DOI: 10.1016/j.ejphar.2018.08.021] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 02/08/2023]
Abstract
Addition of chemical tags on the DNA and modification of histone proteins impart a distinct feature on chromatin architecture. With the advancement in scientific research, the key players underlying these changes have been identified as epigenetic modifiers of the chromatin. Indeed, the plethora of enzymes catalyzing these modifications, portray the diversity of epigenetic space and the intricacy in regulating gene expression. These epigenetic players are categorized as writers: that introduce various chemical modifications on DNA and histones, readers: the specialized domain containing proteins that identify and interpret those modifications and erasers: the dedicated group of enzymes proficient in removing these chemical tags. Research over the past few decades has established that these epigenetic tools are associated with numerous disease conditions especially cancer. Besides, with the involvement of epigenetics in cancer, these enzymes and protein domains provide new targets for cancer drug development. This is certain from the volume of epigenetic research conducted in universities and R&D sector of pharmaceutical industry. Here we have highlighted the different types of epigenetic enzymes and protein domains with an emphasis on methylation and acetylation. This review also deals with the recent developments in small molecule inhibitors as potential anti-cancer drugs targeting the epigenetic space.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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34
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Laskowski D, Humblot P, Sirard MA, Sjunnesson Y, Jhamat N, Båge R, Andersson G. DNA methylation pattern of bovine blastocysts associated with hyperinsulinemia in vitro. Mol Reprod Dev 2018; 85:599-611. [PMID: 29745447 DOI: 10.1002/mrd.22995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/09/2018] [Indexed: 12/22/2022]
Abstract
Insulin functions as a regulator of metabolism and plays an important role in reproduction. Hyperinsulinemia is often observed in patients with obesity and diabetes type 2 and is known to impair fertility, but the underlying molecular mechanisms are only partly understood. Metabolic programming through epigenetic mechanisms such as DNA methylation during embryonic development can lead to health implications for the offspring later in life. Our aim was to study the potential effect of hyperinsulinemia on gene expression and DNA methylation of embryos by adding insulin (0.1 µg/ml = INS0.1 or 10 µg/ml = INS10) during in vitro oocyte maturation by using the EmbryoGENE DNA methylation array for a study of the bovine epigenome. Our results showed significant differences between blastocysts originating from insulin-treated oocytes compared with untreated control blastocysts. In total, 13,658 and 12,418 probes were differentially methylated (DM) in INS0.1 and INS10, respectively, with an overlap of 3,233 probes in the DM regions (DMR) for both insulin groups. Genes related to pathways such as lipid metabolism, growth and proliferation, mitochondrial function, and oxidative stress responses were influenced at both the epigenetic and transcriptomic levels. In addition, imprinted genes and genes with functions in the epigenetic machinery were among the DMRs. This study identified DMRs correlated to differential expression of genes involved in metabolic regulation and should help to improve our knowledge of the underlying molecular mechanisms of metabolic imbalance.
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Affiliation(s)
- Denise Laskowski
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Patrice Humblot
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Marc-André Sirard
- Departement des Sciences Animales, Centre de Recherche en Développement Reproduction et Santé Intergénérationnelle (CRDSI) Pavillon Des Services, University Laval, Québec, Canada
| | - Ylva Sjunnesson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Naveed Jhamat
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Renée Båge
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden
| | - Göran Andersson
- The Centre for Reproductive Biology in Uppsala (CRU), Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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35
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Sasidharan Nair V, El Salhat H, Taha RZ, John A, Ali BR, Elkord E. DNA methylation and repressive H3K9 and H3K27 trimethylation in the promoter regions of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, and PD-L1 genes in human primary breast cancer. Clin Epigenetics 2018; 10:78. [PMID: 29983831 PMCID: PMC6003083 DOI: 10.1186/s13148-018-0512-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/04/2018] [Indexed: 02/08/2023] Open
Abstract
Background High expression of immune checkpoints in tumor microenvironment plays significant roles in inhibiting anti-tumor immunity, which is associated with poor prognosis and cancer progression. Major epigenetic modifications in both DNA and histone could be involved in upregulation of immune checkpoints in cancer. Methods Expressions of different immune checkpoint genes and PD-L1 were assessed using qRT-PCR, and the underlying epigenetic modifications including CpG methylation and repressive histone abundance were determined using bisulfite sequencing, and histone 3 lysine 9 trimethylation (H3K9me3) and histone 3 lysine 27 trimethylation (H3K27me3) chromatin immunoprecipitation assays (ChIP), respectively. Results We first assessed the expression level of six immune checkpoints/ligands and found that PD-1, CTLA-4, TIM-3, and LAG-3 were significantly upregulated in breast tumor tissues (TT), compared with breast normal tissues (NT). We investigated the epigenetic modifications beyond this upregulation in immune checkpoint genes. Interestingly, we found that CpG islands in the promoter regions of PD-1, CTLA-4, and TIM-3 were significantly hypomethylated in tumor compared with normal tissues. Additionally, CpG islands of PD-L1 promoter were completely demethylated (100%), LAG-3 were highly hypomethylated (80–90%), and TIGIT were poorly hypomethylated (20–30%), in both NT and TT. These demethylation findings are in accordance with the relative expression data that, out of all these genes, PD-L1 was highly expressed and completely demethylated and TIGIT was poorly expressed and hypermethylated in both NT and TT. Moreover, bindings of H3K9me3 and H3K27me3 were found to be reduced in the promoter loci of PD-1, CTLA-4, TIM-3, and LAG-3 in tumor tissues. Conclusion Our data demonstrate that both DNA and histone modifications are involved in upregulation of PD-1, CTLA-4, TIM-3, and LAG-3 in breast tumor tissue and these epigenetic modifications could be useful as diagnostic/prognostic biomarkers and/or therapeutic targets in breast cancer. Electronic supplementary material The online version of this article (10.1186/s13148-018-0512-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Varun Sasidharan Nair
- 1Cancer Research Center, Qatar Biomedical Research Institute, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Haytham El Salhat
- 2Oncology Department, Al Noor Hospital, Abu Dhabi, United Arab Emirates.,3Oncology Department, Tawam Hospital, Al Ain, United Arab Emirates
| | - Rowaida Z Taha
- 1Cancer Research Center, Qatar Biomedical Research Institute, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Anne John
- 4Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- 4Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,5Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Eyad Elkord
- 1Cancer Research Center, Qatar Biomedical Research Institute, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.,6Institute of Cancer Sciences, University of Manchester, Manchester, UK
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Stricker SH, Götz M. DNA-Methylation: Master or Slave of Neural Fate Decisions? Front Neurosci 2018; 12:5. [PMID: 29449798 PMCID: PMC5799221 DOI: 10.3389/fnins.2018.00005] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/04/2018] [Indexed: 01/05/2023] Open
Abstract
The pristine formation of complex organs depends on sharp temporal and spatial control of gene expression. Therefore, epigenetic mechanisms have been frequently attributed a central role in controlling cell fate determination. A prime example for this is the first discovered and still most studied epigenetic mark, DNA methylation, and the development of the most complex mammalian organ, the brain. Recently, the field of epigenetics has advanced significantly: new DNA modifications were discovered, epigenomic profiling became widely accessible, and methods for targeted epigenomic manipulation have been developed. Thus, it is time to challenge established models of epigenetic gene regulation. Here, we review the current state of knowledge about DNA modifications, their epigenomic distribution, and their regulatory role. We will summarize the evidence suggesting they possess crucial roles in neurogenesis and discuss whether this likely includes lineage choice regulation or rather effects on differentiation. Finally, we will attempt an outlook on how questions, which remain unresolved, could be answered soon.
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Affiliation(s)
- Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, Munich, Germany.,Physiological Genomics, BioMedical Center, Munich, Germany.,German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Germany and Biomedical Center, Institute of Stem Cell Research, Helmholtz Zentrum, Ludwig-Maximilian-Universität, Munich, Germany
| | - Magdalena Götz
- Physiological Genomics, BioMedical Center, Munich, Germany.,German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Germany and Biomedical Center, Institute of Stem Cell Research, Helmholtz Zentrum, Ludwig-Maximilian-Universität, Munich, Germany.,German Excellence Cluster of Systems Neurology, Munich, Germany
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Kang SW, Madkour M, Kuenzel WJ. Tissue-Specific Expression of DNA Methyltransferases Involved in Early-Life Nutritional Stress of Chicken, Gallus gallus. Front Genet 2017; 8:204. [PMID: 29270191 PMCID: PMC5723639 DOI: 10.3389/fgene.2017.00204] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/22/2017] [Indexed: 12/15/2022] Open
Abstract
DNA methylation was reported as a possible stress-adaptation mechanism involved in the transcriptional regulation of stress responsive genes. Limited data are available on effects of psychological stress and early-life nutritional stress on DNA methylation regulators [DNMTs: DNA (cytosine-5)-methyltransferase 1 (DNMT1), DNMT1 associated protein (DMAP1), DNMT 3 alpha (DNMT3A) and beta (DNMT3B)] in avian species. The objectives of this study were to: (1) investigate changes in expression of DNMT1, DMAP1, DNMT3A, and DNMT3B following acute (AS) or chronic immobilization stress (CS); (2) test immediate effect of early-life nutritional stress [food deprivation (FD) for 12 h (12hFD) or 36 h (36hFD) at the post-hatching period] on expression of DNA methylation regulators and glucocorticoid receptor (GR), and the long-term effect of early-life nutritional stress at 6 weeks of age. Expression of DNMTs and plasma corticosterone (CORT) concentration decreased by CS compared to AS (p < 0.05), indicating differential roles of DNA methylation regulators in the stress response. Plasma CORT at 12hFD and 36hFD birds increased compared to control birds (12hF and 36hF), but there were no significant differences in plasma CORT of 12hFD and 36hFD birds at 6 weeks of age compared to 6 week controls. DNMT1, DMAP1, and DNMT3B expression in the anterior pituitary increased by 12hFD, but decreased at 36hFD compared to their controls (P < 0.05). In liver, DNMT1, DNMT3A, and DNMT3B expression decreased by 12hFD, however, no significant changes occurred at 36hFD. Expression of DMAP1, DNMT3A, and DNMT3B in anterior pituitary and DMAP1 and DNMT3A expression in liver at 6 weeks of age were higher in 36hFD stressed birds compared to controls as well as 12hFD stressed birds. Hepatic GR expression decreased by 12hFD and increased by 36hFD (p < 0.05). Expression patterns of GR in the liver of FD stress-induced birds persisted until 6 weeks of age, suggesting the possible lifelong involvement of liver GR in early-life nutritional stress response of birds. Taken together, results suggest that DNA methylation regulator genes are tissue-specifically responsive to acute and chronic stress, and hepatic GR may play a critical role in regulating the early-life nutritional stress response of birds. In addition, the downregulation of DNMT1 and DMAP1 may be one of the adaptive mechanisms to chronic early-life nutritional stress via passive demethylation.
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Affiliation(s)
- Seong W. Kang
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, FayettevilleAR, United States
| | - Mahmoud Madkour
- Department of Animal Production, National Research CenterGiza, Egypt
| | - Wayne J. Kuenzel
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, FayettevilleAR, United States
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Abstract
Purpose The focus of this review is to provide an overview of the recent findings on the role of epigenetic mechanisms in periodontal disease, including disease susceptibility, progression, and as potential treatment options. Recent Findings The findings on the influence of oral pathogens on epigenetic regulation of pathogen recognition receptors, such as Toll-like receptors, as well as pro-inflammatory cytokines suggest an important role for epigenetics in the regulation of the host immune response. Recent studies also show that the epigenetic pattern in periodontitis lesions differ from that of healthy and gingivitis tissue. In addition, these patterns differ between tissues in the same individual. Research is also indicating a role for both DNA methylation and histone acetylation on cells osteogenic differentiation and bone regeneration. Summary Knowledge of epigenetic pattern in periodontal diseases may add not only to the knowledge of susceptibility of the disease but may also be a diagnostic tool to identify patients at risk to develop the severe form of periodontitis. In addition, recent research within gene therapy and tissue engineering indicate a role for epigenetics also to improve regeneration of periodontal tissues.
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Affiliation(s)
- Lena Larsson
- Department of Periodontology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Box 450, SE-405 30 Gothenburg, Sweden
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Feroe A, Broene R, Albuquerque D, Ruiz P. Endocrine Disrupting Chemicals, Transgenerational Epigenetics and Metabolic Diseases. EC ENDOCRINOLOGY AND METABOLIC RESEARCH 2017; 21:31-51. [PMID: 34734213 PMCID: PMC8563023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Exposure to environmental chemicals can produce effects on the endocrine system through epigenetic mechanisms. These can considerably decrease or increase the sensitivity of multiple hormones depending on the dose, route, or time of exposure. The exposure of endocrine disrupting chemicals (EDCs) during the in utero period could be a critical window, altering the epigenome profile. Recently, several researchers suggest a role of EDCs in the obesity epidemic. In this brief review, we focused on how four EDCs (bisphenol A, dichlorodiphenyltrichloroethane, di-(2-ethylhexyl) phthalate and tributyltin) may underlay transgenerational epigenetic effects. We also discuss the adipogenesis signaling pathway and the impact of exposure to individual or mixtures of EDCs on the developing endocrine system. Understanding the molecular determinants of epigenetic memory across generations will provide essential insight into how environmental exposure can affect the health of individuals, as well as subsequent generations.
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Affiliation(s)
| | - Richard Broene
- Department of Chemistry, Bowdoin College, Brunswick, ME, USA
| | - David Albuquerque
- Research Center for Anthropology and Health, University of Coimbra, Coimbra, Portugal
| | - Patricia Ruiz
- Division of Toxicology and Human Health Sciences, Agency for Toxic Substances and Disease Registry, Atlanta, Georgia
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Diomede F, Thangavelu SR, Merciaro I, D'Orazio M, Bramanti P, Mazzon E, Trubiani O. Porphyromonas gingivalis lipopolysaccharide stimulation in human periodontal ligament stem cells: role of epigenetic modifications to the inflammation. Eur J Histochem 2017; 61:2826. [PMID: 29046054 PMCID: PMC5575416 DOI: 10.4081/ejh.2017.2826] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
Periodontitis is a chronic oral inflammatory disease produced by bacteria. Gingival retraction and bone and connective tissues resorption are the hallmarks of this disease. Chronic periodontitis may contribute to the risk of onset or progression of neuroinflammatory pathological conditions, such as Alzheimer’s disease. The main goal of the present study was to investigate if the role of epigenetic modulations is involved in periodontitis using human periodontal ligament stem cells (hPDLSCs) as an in vitro model system. hPDLSCs were treated with lipopolysaccharide of Porphyromonas gingivalis and the expression of proteins associated with DNA methylation and histone acetylation, such as DNMT1 and p300, respectively, and inflammatory transcription factor NF-kB, were examined. Immunofluorescence, Western blot and next generation sequencing results demonstrated that P. gingivalis lipopolysaccharide significantly reduced DNA methylase DNMT1, while it markedly upregulated the level of histone acetyltransferase p300 and NF-kB in hPDLSCs. Our results showed that P. gingivalis lipopolysaccharide markedly regulate the genes involved in epigenetic mechanism, which may result in inflammation induction. We propose that P. gingivalis lipopolysaccharide-treated hPDLSCs could be a potential in vitro model system to study epigenetics modulations associated with periodontitis, which might be helpful to identify novel biomarkers linked to this oral inflammatory disease.
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Affiliation(s)
- Francesca Diomede
- University "G. d'Annunzio", Department of Medical, Oral and Biotechnological Sciences.
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41
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Sadakierska-Chudy A, Frankowska M, Wydra K, Jastrzębska J, Miszkiel J, Filip M. Increased 5-hydroxymethylation levels in the hippocampus of rat extinguished from cocaine self-administration. Hippocampus 2017; 27:811-821. [PMID: 28422379 DOI: 10.1002/hipo.22733] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/09/2017] [Accepted: 04/12/2017] [Indexed: 12/25/2022]
Abstract
Drug craving and relapse risk during abstinence from cocaine are thought to be caused by persistent changes in transcription and chromatin regulation. Although several brain regions are involved in these processes, the hippocampus seems to play an important role in context-evoked craving and drug-seeking behavior. Only a few studies have examined epigenetic alterations during a period of cocaine abstinence. To investigate the effects of cocaine abstinence on DNA methylation and gene expression, rats that self-administered the drug underwent cocaine abstinence in two time points with extinction training. During the cocaine extinction, we observed elevated global 5-hydroxymethylcytosine(5-hmC) levels with a concurrent increase in Tet3 transcript levels. Moreover, we did not find significant alterations in the levels of Tet3 mRNA and 5-hmC in rats subjected to cocaine abstinence without extinction training. Additionally, our findings demonstrated that the expression of Tet3 target genes was activated. Besides, altered DNA methylation was detected at promoter regions of miRNAs, such as miR-30d and miR-let7i. Further in silico analysis provided evidence that these two molecules targeted the 3' UTR region of the Tet3 gene and thus may contribute to its post-transcriptional regulation. This study has presented novel findings in the hippocampus of rats that underwent extinction training following cocaine self-administration. The alterations in the Tet3 gene expression and the level of 5-hmC may play an important role in extinction learning and the reduction of subsequent cocaine seeking.
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Affiliation(s)
- Anna Sadakierska-Chudy
- Department of Pharmacology, Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, ul. Smetna 12, Krakow, 31-343, Poland
| | - Małgorzata Frankowska
- Department of Pharmacology, Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, ul. Smetna 12, Krakow, 31-343, Poland
| | - Karolina Wydra
- Department of Pharmacology, Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, ul. Smetna 12, Krakow, 31-343, Poland
| | - Joanna Jastrzębska
- Department of Pharmacology, Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, ul. Smetna 12, Krakow, 31-343, Poland
| | - Joanna Miszkiel
- Department of Pharmacology, Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, ul. Smetna 12, Krakow, 31-343, Poland
| | - Małgorzata Filip
- Department of Pharmacology, Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, ul. Smetna 12, Krakow, 31-343, Poland
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Lussier AA, Weinberg J, Kobor MS. Epigenetics studies of fetal alcohol spectrum disorder: where are we now? Epigenomics 2017; 9:291-311. [PMID: 28234026 PMCID: PMC5549650 DOI: 10.2217/epi-2016-0163] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Adverse in utero events can alter the development and function of numerous physiological systems, giving rise to lasting neurodevelopmental deficits. In particular, data have shown that prenatal alcohol exposure can reprogram neurobiological systems, altering developmental trajectories and resulting in increased vulnerability to adverse neurobiological, behavioral and health outcomes. Increasing evidence suggests that epigenetic mechanisms are potential mediators for the reprogramming of neurobiological systems, as they may provide a link between the genome, environmental conditions and neurodevelopmental outcomes. This review outlines the current state of epigenetic research in fetal alcohol spectrum disorder, highlighting the role of epigenetic mechanisms in the reprogramming of neurobiological systems by alcohol and as potential diagnostic tools for fetal alcohol spectrum disorder. We also present an assessment of the current limitations in studies of prenatal alcohol exposure, and highlight the future steps needed in the field.
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Affiliation(s)
- Alexandre A Lussier
- Department of Medical Genetics, Centre for Molecular Medicine & Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Cellular & Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joanne Weinberg
- Department of Cellular & Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine & Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, British Columbia, Canada
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Rea M, Eckstein M, Eleazer R, Smith C, Fondufe-Mittendorf YN. Genome-wide DNA methylation reprogramming in response to inorganic arsenic links inhibition of CTCF binding, DNMT expression and cellular transformation. Sci Rep 2017; 7:41474. [PMID: 28150704 PMCID: PMC5288714 DOI: 10.1038/srep41474] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022] Open
Abstract
Chronic low dose inorganic arsenic (iAs) exposure leads to changes in gene expression and epithelial-to-mesenchymal transformation. During this transformation, cells adopt a fibroblast-like phenotype accompanied by profound gene expression changes. While many mechanisms have been implicated in this transformation, studies that focus on the role of epigenetic alterations in this process are just emerging. DNA methylation controls gene expression in physiologic and pathologic states. Several studies show alterations in DNA methylation patterns in iAs-mediated pathogenesis, but these studies focused on single genes. We present a comprehensive genome-wide DNA methylation analysis using methyl-sequencing to measure changes between normal and iAs-transformed cells. Additionally, these differential methylation changes correlated positively with changes in gene expression and alternative splicing. Interestingly, most of these differentially methylated genes function in cell adhesion and communication pathways. To gain insight into how genomic DNA methylation patterns are regulated during iAs-mediated carcinogenesis, we show that iAs probably targets CTCF binding at the promoter of DNA methyltransferases, regulating their expression. These findings reveal how CTCF binding regulates DNA methyltransferase to reprogram the methylome in response to an environmental toxin.
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Affiliation(s)
- Matthew Rea
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Meredith Eckstein
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Rebekah Eleazer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Caroline Smith
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA.,Bellarmine University, Louisville, KY 40205, USA
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Kejík Z, Kaplánek R, Havlík M, Bříza T, Jakubek M, Králová J, Mikula I, Martásek P, Král V. Optical probes and sensors as perspective tools in epigenetics. Bioorg Med Chem 2017; 25:2295-2306. [PMID: 28285925 DOI: 10.1016/j.bmc.2017.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/13/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022]
Abstract
Modifications of DNA cytosine bases and histone posttranslational modifications play key roles in the control of gene expression and specification of cell states. Such modifications affect many important biological processes and changes to these important regulation mechanisms can initiate or significantly contribute to the development of many serious pathological states. Therefore, recognition and determination of chromatin modifications is an important goal in basic and clinical research. Two of the most promising tools for this purpose are optical probes and sensors, especially colourimetric and fluorescence devices. The use of optical probes and sensors is simple, without highly expensive instrumentation, and with excellent sensitivity and specificity for target structural motifs. Accordingly, the application of various probes and sensors in the recognition and determination of cytosine modifications and structure of histones and histone posttranslational modifications, are discussed in detail in this review.
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Affiliation(s)
- Zdeněk Kejík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Robert Kaplánek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Martin Havlík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Tomáš Bříza
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Milan Jakubek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Jarmila Králová
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Ivan Mikula
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Pavel Martásek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Vladimír Král
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic.
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45
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Navarro E, Funtikova AN, Fíto M, Schröder H. Prenatal nutrition and the risk of adult obesity: Long-term effects of nutrition on epigenetic mechanisms regulating gene expression. J Nutr Biochem 2017; 39:1-14. [DOI: 10.1016/j.jnutbio.2016.03.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 03/23/2016] [Accepted: 03/27/2016] [Indexed: 12/19/2022]
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46
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Huang Z, Huang Q, Ji L, Wang Y, Qi X, Liu L, Liu Z, Lu L. Epigenetic regulation of active Chinese herbal components for cancer prevention and treatment: A follow-up review. Pharmacol Res 2016; 114:1-12. [PMID: 27697644 DOI: 10.1016/j.phrs.2016.09.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/13/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022]
Abstract
Epigenetic modifications include DNA methylation, histone modification, and other patterns. These processes are associated with carcinogenesis and cancer progression. Thus, epigenetic modification-related enzymes, such as DNA methyltransferases (DNMTs), histone methyltransferases (HMTs), histone demethylases (HDMTs), histone acetyltransferases (HATs), and histone deacetylases (HDACs), as well as some related proteins, including methyl-CpG binding proteins (MBPs) and DNMT1-associated protein (DMAP 1), are considered as potential targets for cancer prevention and therapy. Numerous natural compounds, mainly derived from Chinese herbs and chemically ranging from polyphenols and flavonoids to mineral salts, inhibit the growth and development of various cancers by targeting multiple genetic and epigenetic alterations. This review summarizes the epigenetic mechanisms by which active compounds from Chinese herbs exert their anti-cancer effect. A subset of these compounds, such as curcumin and resveratrol, affect multiple epigenetic processes, including DNMT inhibition, HDAC inactivation, MBP suppression, HAT activation, and microRNA modulation. Other compounds also regulate epigenetic modification processes, but the underlying mechanisms and clear targets remain unknown. Accordingly, further studies are required.
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Affiliation(s)
- Zhiying Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Qiuju Huang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Liyan Ji
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Ying Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Xiaoxiao Qi
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR), China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR), China.
| | - Linlin Lu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR), China.
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47
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Tebani A, Afonso C, Marret S, Bekri S. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations. Int J Mol Sci 2016; 17:ijms17091555. [PMID: 27649151 PMCID: PMC5037827 DOI: 10.3390/ijms17091555] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022] Open
Abstract
The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM) are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.
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Affiliation(s)
- Abdellah Tebani
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031 Rouen, France.
- Normandie University, UNIROUEN, INSERM, CHU Rouen, Laboratoire NeoVasc ERI28, 76000 Rouen, France.
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Carlos Afonso
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Stéphane Marret
- Normandie University, UNIROUEN, INSERM, CHU Rouen, Laboratoire NeoVasc ERI28, 76000 Rouen, France.
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Rouen University Hospital, 76031 Rouen, France.
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031 Rouen, France.
- Normandie University, UNIROUEN, INSERM, CHU Rouen, Laboratoire NeoVasc ERI28, 76000 Rouen, France.
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48
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Sipilä P, Björkgren I. Segment-specific regulation of epididymal gene expression. Reproduction 2016; 152:R91-9. [DOI: 10.1530/rep-15-0533] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 05/23/2016] [Indexed: 01/24/2023]
Abstract
The epididymis is necessary for post-testicular sperm maturation. During their epididymal transit, spermatozoa gain ability for progressive movement and fertilization. The epididymis is composed of several segments that have distinct gene expression profiles that enable the establishment of the changing luminal environment required for sperm maturation. The epididymal gene expression is regulated by endocrine, lumicrine, and paracrine factors in a segment-specific manner. Thus, in addition to its importance for male fertility, the epididymis is a valuable model tissue for studying the regulation of gene expression. This review concentrates on recent advances in understanding the androgen, small RNA, and epigenetically mediated regulation of segment-specific gene expression in the epididymis.
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49
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Fries GR, Li Q, McAlpin B, Rein T, Walss-Bass C, Soares JC, Quevedo J. The role of DNA methylation in the pathophysiology and treatment of bipolar disorder. Neurosci Biobehav Rev 2016; 68:474-488. [PMID: 27328785 DOI: 10.1016/j.neubiorev.2016.06.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/03/2016] [Accepted: 06/12/2016] [Indexed: 12/31/2022]
Abstract
Bipolar disorder (BD) is a multifactorial illness thought to result from an interaction between genetic susceptibility and environmental stimuli. Epigenetic mechanisms, including DNA methylation, can modulate gene expression in response to the environment, and therefore might account for part of the heritability reported for BD. This paper aims to review evidence of the potential role of DNA methylation in the pathophysiology and treatment of BD. In summary, several studies suggest that alterations in DNA methylation may play an important role in the dysregulation of gene expression in BD, and some actually suggest their potential use as biomarkers to improve diagnosis, prognosis, and assessment of response to treatment. This is also supported by reports of alterations in the levels of DNA methyltransferases in patients and in the mechanism of action of classical mood stabilizers. In this sense, targeting specific alterations in DNA methylation represents exciting new treatment possibilities for BD, and the 'plastic' characteristic of DNA methylation accounts for a promising possibility of restoring environment-induced modifications in patients.
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Affiliation(s)
- Gabriel R Fries
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA.
| | - Qiongzhen Li
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA
| | - Blake McAlpin
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA
| | - Theo Rein
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstraße 2-10, 80804, Munich, Germany
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Jair C Soares
- Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA; Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA; Laboratory of Neurosciences, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
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50
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Chaitankar V, Karakülah G, Ratnapriya R, Giuste FO, Brooks MJ, Swaroop A. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res 2016; 55:1-31. [PMID: 27297499 DOI: 10.1016/j.preteyeres.2016.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 02/08/2023]
Abstract
The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well.
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Affiliation(s)
- Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Gökhan Karakülah
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Felipe O Giuste
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Matthew J Brooks
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
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